Biofuels and other renewable fossil fuel substitutes are attracting great interest, due to concerns about future availability of fossil fuels. In addition, concerns about climate change have sparked interest in schemes to reduce the emission of carbon into the atmosphere. One potential way to address these problems is to inject carbon into biofuel manufacturing processes in order to capture the carbon. However, biological uptake of carbon materials injected into biofuel manufacturing plants is not well understood. Accordingly, there is a need for improved methods and systems for utilizing carbon emissions in biofuel manufacturing processes.